Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/pydot.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
parents
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4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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1 """An interface to GraphViz."""
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2 from __future__ import division
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3 from __future__ import print_function
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4 import copy
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5 import io
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6 import errno
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7 import os
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8 import re
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9 import subprocess
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10 import sys
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11 import tempfile
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12 import warnings
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13
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14 try:
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15 import dot_parser
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16 except Exception as e:
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17 warnings.warn(
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18 "`pydot` could not import `dot_parser`, "
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19 "so `pydot` will be unable to parse DOT files. "
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20 "The error was: {e}".format(e=e))
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21
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22
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23 __author__ = 'Ero Carrera'
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24 __version__ = '1.4.2'
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25 __license__ = 'MIT'
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26
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27
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28 PY3 = sys.version_info >= (3, 0, 0)
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29 if PY3:
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30 str_type = str
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31 else:
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32 str_type = basestring
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33
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34
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35 GRAPH_ATTRIBUTES = { 'Damping', 'K', 'URL', 'aspect', 'bb', 'bgcolor',
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36 'center', 'charset', 'clusterrank', 'colorscheme', 'comment', 'compound',
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37 'concentrate', 'defaultdist', 'dim', 'dimen', 'diredgeconstraints',
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38 'dpi', 'epsilon', 'esep', 'fontcolor', 'fontname', 'fontnames',
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39 'fontpath', 'fontsize', 'id', 'label', 'labeljust', 'labelloc',
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40 'landscape', 'layers', 'layersep', 'layout', 'levels', 'levelsgap',
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41 'lheight', 'lp', 'lwidth', 'margin', 'maxiter', 'mclimit', 'mindist',
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42 'mode', 'model', 'mosek', 'nodesep', 'nojustify', 'normalize', 'nslimit',
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43 'nslimit1', 'ordering', 'orientation', 'outputorder', 'overlap',
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44 'overlap_scaling', 'pack', 'packmode', 'pad', 'page', 'pagedir',
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45 'quadtree', 'quantum', 'rankdir', 'ranksep', 'ratio', 'remincross',
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46 'repulsiveforce', 'resolution', 'root', 'rotate', 'searchsize', 'sep',
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47 'showboxes', 'size', 'smoothing', 'sortv', 'splines', 'start',
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48 'stylesheet', 'target', 'truecolor', 'viewport', 'voro_margin',
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49 # for subgraphs
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50 'rank' }
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51
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52
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53 EDGE_ATTRIBUTES = { 'URL', 'arrowhead', 'arrowsize', 'arrowtail',
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54 'color', 'colorscheme', 'comment', 'constraint', 'decorate', 'dir',
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55 'edgeURL', 'edgehref', 'edgetarget', 'edgetooltip', 'fontcolor',
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56 'fontname', 'fontsize', 'headURL', 'headclip', 'headhref', 'headlabel',
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57 'headport', 'headtarget', 'headtooltip', 'href', 'id', 'label',
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58 'labelURL', 'labelangle', 'labeldistance', 'labelfloat', 'labelfontcolor',
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59 'labelfontname', 'labelfontsize', 'labelhref', 'labeltarget',
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60 'labeltooltip', 'layer', 'len', 'lhead', 'lp', 'ltail', 'minlen',
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61 'nojustify', 'penwidth', 'pos', 'samehead', 'sametail', 'showboxes',
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62 'style', 'tailURL', 'tailclip', 'tailhref', 'taillabel', 'tailport',
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63 'tailtarget', 'tailtooltip', 'target', 'tooltip', 'weight',
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64 'rank' }
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65
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66
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67 NODE_ATTRIBUTES = { 'URL', 'color', 'colorscheme', 'comment',
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68 'distortion', 'fillcolor', 'fixedsize', 'fontcolor', 'fontname',
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69 'fontsize', 'group', 'height', 'id', 'image', 'imagescale', 'label',
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70 'labelloc', 'layer', 'margin', 'nojustify', 'orientation', 'penwidth',
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71 'peripheries', 'pin', 'pos', 'rects', 'regular', 'root', 'samplepoints',
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72 'shape', 'shapefile', 'showboxes', 'sides', 'skew', 'sortv', 'style',
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73 'target', 'tooltip', 'vertices', 'width', 'z',
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74 # The following are attributes dot2tex
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75 'texlbl', 'texmode' }
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76
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77
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78 CLUSTER_ATTRIBUTES = { 'K', 'URL', 'bgcolor', 'color', 'colorscheme',
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79 'fillcolor', 'fontcolor', 'fontname', 'fontsize', 'label', 'labeljust',
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80 'labelloc', 'lheight', 'lp', 'lwidth', 'nojustify', 'pencolor',
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81 'penwidth', 'peripheries', 'sortv', 'style', 'target', 'tooltip' }
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82
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83
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84 DEFAULT_PROGRAMS = {
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85 'dot',
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86 'twopi',
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87 'neato',
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88 'circo',
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89 'fdp',
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90 'sfdp',
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91 }
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92
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93
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94 def is_windows():
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95 # type: () -> bool
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96 return os.name == 'nt'
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97
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98
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99 def is_anaconda():
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100 # type: () -> bool
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101 import glob
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102 return glob.glob(os.path.join(sys.prefix, 'conda-meta\\graphviz*.json')) != []
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103
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104
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105 def get_executable_extension():
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106 # type: () -> str
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107 if is_windows():
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108 return '.bat' if is_anaconda() else '.exe'
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109 else:
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110 return ''
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111
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112
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113 def call_graphviz(program, arguments, working_dir, **kwargs):
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114 # explicitly inherit `$PATH`, on Windows too,
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115 # with `shell=False`
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116
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117 if program in DEFAULT_PROGRAMS:
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118 extension = get_executable_extension()
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119 program += extension
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120
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121 if arguments is None:
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122 arguments = []
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123
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124 env = {
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125 'PATH': os.environ.get('PATH', ''),
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126 'LD_LIBRARY_PATH': os.environ.get('LD_LIBRARY_PATH', ''),
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127 'SYSTEMROOT': os.environ.get('SYSTEMROOT', ''),
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128 }
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129
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130 program_with_args = [program, ] + arguments
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131
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132 process = subprocess.Popen(
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133 program_with_args,
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134 env=env,
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135 cwd=working_dir,
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136 shell=False,
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137 stderr=subprocess.PIPE,
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138 stdout=subprocess.PIPE,
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139 **kwargs
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140 )
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141 stdout_data, stderr_data = process.communicate()
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142
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143 return stdout_data, stderr_data, process
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144
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145
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146 #
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147 # Extended version of ASPN's Python Cookbook Recipe:
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148 # Frozen dictionaries.
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149 # https://code.activestate.com/recipes/414283/
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150 #
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151 # This version freezes dictionaries used as values within dictionaries.
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152 #
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153 class frozendict(dict):
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154 def _blocked_attribute(obj):
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155 raise AttributeError('A frozendict cannot be modified.')
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156 _blocked_attribute = property(_blocked_attribute)
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157
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158 __delitem__ = __setitem__ = clear = _blocked_attribute
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159 pop = popitem = setdefault = update = _blocked_attribute
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160
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161 def __new__(cls, *args, **kw):
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162 new = dict.__new__(cls)
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163
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164 args_ = []
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165 for arg in args:
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166 if isinstance(arg, dict):
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167 arg = copy.copy(arg)
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168 for k in arg:
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169 v = arg[k]
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170 if isinstance(v, frozendict):
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171 arg[k] = v
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172 elif isinstance(v, dict):
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173 arg[k] = frozendict(v)
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174 elif isinstance(v, list):
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175 v_ = list()
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176 for elm in v:
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177 if isinstance(elm, dict):
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178 v_.append( frozendict(elm) )
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179 else:
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180 v_.append( elm )
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181 arg[k] = tuple(v_)
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182 args_.append( arg )
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183 else:
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184 args_.append( arg )
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185
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186 dict.__init__(new, *args_, **kw)
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187 return new
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188
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189 def __init__(self, *args, **kw):
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190 pass
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191
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192 def __hash__(self):
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193 try:
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194 return self._cached_hash
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195 except AttributeError:
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196 h = self._cached_hash = hash(tuple(sorted(self.items())))
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197 return h
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198
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199 def __repr__(self):
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200 return "frozendict(%s)" % dict.__repr__(self)
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201
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202
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203 dot_keywords = ['graph', 'subgraph', 'digraph', 'node', 'edge', 'strict']
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204
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205 id_re_alpha_nums = re.compile('^[_a-zA-Z][a-zA-Z0-9_,]*$', re.UNICODE)
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206 id_re_alpha_nums_with_ports = re.compile(
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207 '^[_a-zA-Z][a-zA-Z0-9_,:\"]*[a-zA-Z0-9_,\"]+$', re.UNICODE)
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208 id_re_num = re.compile('^[0-9,]+$', re.UNICODE)
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209 id_re_with_port = re.compile('^([^:]*):([^:]*)$', re.UNICODE)
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210 id_re_dbl_quoted = re.compile('^\".*\"$', re.S|re.UNICODE)
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211 id_re_html = re.compile('^<.*>$', re.S|re.UNICODE)
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212
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213
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214 def needs_quotes( s ):
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215 """Checks whether a string is a dot language ID.
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216
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217 It will check whether the string is solely composed
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218 by the characters allowed in an ID or not.
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219 If the string is one of the reserved keywords it will
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220 need quotes too but the user will need to add them
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221 manually.
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222 """
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223
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224 # If the name is a reserved keyword it will need quotes but pydot
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225 # can't tell when it's being used as a keyword or when it's simply
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226 # a name. Hence the user needs to supply the quotes when an element
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227 # would use a reserved keyword as name. This function will return
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228 # false indicating that a keyword string, if provided as-is, won't
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229 # need quotes.
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230 if s in dot_keywords:
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231 return False
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232
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233 chars = [ord(c) for c in s if ord(c)>0x7f or ord(c)==0]
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234 if chars and not id_re_dbl_quoted.match(s) and not id_re_html.match(s):
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235 return True
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236
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237 for test_re in [id_re_alpha_nums, id_re_num,
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238 id_re_dbl_quoted, id_re_html,
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239 id_re_alpha_nums_with_ports]:
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240 if test_re.match(s):
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241 return False
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242
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243 m = id_re_with_port.match(s)
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244 if m:
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245 return needs_quotes(m.group(1)) or needs_quotes(m.group(2))
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246
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247 return True
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248
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249
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250 def quote_if_necessary(s):
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251 """Enclose attribute value in quotes, if needed."""
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252 if isinstance(s, bool):
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253 if s is True:
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254 return 'True'
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255 return 'False'
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256
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257 if not isinstance( s, str_type):
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258 return s
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259
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260 if not s:
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261 return s
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262
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263 if needs_quotes(s):
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264 replace = {'"' : r'\"',
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265 "\n" : r'\n',
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266 "\r" : r'\r'}
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267 for (a,b) in replace.items():
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268 s = s.replace(a, b)
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269
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270 return '"' + s + '"'
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271
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272 return s
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273
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274
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275
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276 def graph_from_dot_data(s):
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277 """Load graphs from DOT description in string `s`.
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278
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279 @param s: string in [DOT language](
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280 https://en.wikipedia.org/wiki/DOT_(graph_description_language))
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281
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282 @return: Graphs that result from parsing.
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283 @rtype: `list` of `pydot.Dot`
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284 """
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285 return dot_parser.parse_dot_data(s)
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286
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287
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288 def graph_from_dot_file(path, encoding=None):
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289 """Load graphs from DOT file at `path`.
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290
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291 @param path: to DOT file
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292 @param encoding: as passed to `io.open`.
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293 For example, `'utf-8'`.
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294
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295 @return: Graphs that result from parsing.
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296 @rtype: `list` of `pydot.Dot`
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297 """
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298 with io.open(path, 'rt', encoding=encoding) as f:
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299 s = f.read()
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300 if not PY3:
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301 s = unicode(s)
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302 graphs = graph_from_dot_data(s)
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303 return graphs
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304
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305
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306
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307 def graph_from_edges(edge_list, node_prefix='', directed=False):
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308 """Creates a basic graph out of an edge list.
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309
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310 The edge list has to be a list of tuples representing
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311 the nodes connected by the edge.
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312 The values can be anything: bool, int, float, str.
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313
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314 If the graph is undirected by default, it is only
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315 calculated from one of the symmetric halves of the matrix.
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316 """
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317
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318 if directed:
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319 graph = Dot(graph_type='digraph')
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320
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321 else:
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322 graph = Dot(graph_type='graph')
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323
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324 for edge in edge_list:
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325
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326 if isinstance(edge[0], str):
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327 src = node_prefix + edge[0]
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328 else:
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329 src = node_prefix + str(edge[0])
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330
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331 if isinstance(edge[1], str):
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332 dst = node_prefix + edge[1]
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333 else:
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334 dst = node_prefix + str(edge[1])
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335
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336 e = Edge( src, dst )
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337 graph.add_edge(e)
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338
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339 return graph
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340
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341
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342 def graph_from_adjacency_matrix(matrix, node_prefix= u'', directed=False):
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343 """Creates a basic graph out of an adjacency matrix.
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344
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345 The matrix has to be a list of rows of values
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346 representing an adjacency matrix.
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347 The values can be anything: bool, int, float, as long
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348 as they can evaluate to True or False.
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349 """
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350
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351 node_orig = 1
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352
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353 if directed:
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354 graph = Dot(graph_type='digraph')
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355 else:
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356 graph = Dot(graph_type='graph')
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357
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358 for row in matrix:
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359 if not directed:
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360 skip = matrix.index(row)
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361 r = row[skip:]
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362 else:
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363 skip = 0
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364 r = row
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365 node_dest = skip+1
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366
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367 for e in r:
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368 if e:
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369 graph.add_edge(
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370 Edge('%s%s' % (node_prefix, node_orig),
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371 '%s%s' % (node_prefix, node_dest)))
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372 node_dest += 1
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373 node_orig += 1
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374
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375 return graph
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376
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377
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378 def graph_from_incidence_matrix(matrix, node_prefix='', directed=False):
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379 """Creates a basic graph out of an incidence matrix.
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380
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381 The matrix has to be a list of rows of values
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382 representing an incidence matrix.
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383 The values can be anything: bool, int, float, as long
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384 as they can evaluate to True or False.
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385 """
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386
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387 node_orig = 1
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388
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389 if directed:
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390 graph = Dot(graph_type='digraph')
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391 else:
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392 graph = Dot(graph_type='graph')
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393
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394 for row in matrix:
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395 nodes = []
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396 c = 1
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397
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398 for node in row:
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399 if node:
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400 nodes.append(c*node)
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401 c += 1
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402 nodes.sort()
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403
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404 if len(nodes) == 2:
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405 graph.add_edge(
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406 Edge('%s%s' % (node_prefix, abs(nodes[0])),
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407 '%s%s' % (node_prefix, nodes[1])))
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408
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409 if not directed:
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410 graph.set_simplify(True)
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411
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412 return graph
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413
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414
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415 class Common(object):
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416 """Common information to several classes.
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417
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418 Should not be directly used, several classes are derived from
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419 this one.
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420 """
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421
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422
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423 def __getstate__(self):
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424
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425 dict = copy.copy(self.obj_dict)
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426
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427 return dict
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428
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429
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430 def __setstate__(self, state):
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431
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432 self.obj_dict = state
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433
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434
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435 def __get_attribute__(self, attr):
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436 """Look for default attributes for this node"""
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437
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438 attr_val = self.obj_dict['attributes'].get(attr, None)
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439
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440 if attr_val is None:
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441 # get the defaults for nodes/edges
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442
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443 default_node_name = self.obj_dict['type']
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444
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445 # The defaults for graphs are set on a node named 'graph'
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446 if default_node_name in ('subgraph', 'digraph', 'cluster'):
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447 default_node_name = 'graph'
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448
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449 g = self.get_parent_graph()
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450 if g is not None:
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451 defaults = g.get_node( default_node_name )
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452 else:
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453 return None
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454
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455 # Multiple defaults could be set by having repeated 'graph [...]'
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456 # 'node [...]', 'edge [...]' statements. In such case, if the
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457 # same attribute is set in different statements, only the first
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458 # will be returned. In order to get all, one would call the
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459 # get_*_defaults() methods and handle those. Or go node by node
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460 # (of the ones specifying defaults) and modify the attributes
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461 # individually.
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462 #
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463 if not isinstance(defaults, (list, tuple)):
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464 defaults = [defaults]
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465
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466 for default in defaults:
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467 attr_val = default.obj_dict['attributes'].get(attr, None)
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468 if attr_val:
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469 return attr_val
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470 else:
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471 return attr_val
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472
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473 return None
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474
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475
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476 def set_parent_graph(self, parent_graph):
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477
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478 self.obj_dict['parent_graph'] = parent_graph
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479
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480
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481 def get_parent_graph(self):
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482
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483 return self.obj_dict.get('parent_graph', None)
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484
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485
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486 def set(self, name, value):
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487 """Set an attribute value by name.
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488
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489 Given an attribute 'name' it will set its value to 'value'.
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490 There's always the possibility of using the methods:
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491
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492 set_'name'(value)
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493
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494 which are defined for all the existing attributes.
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495 """
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496
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497 self.obj_dict['attributes'][name] = value
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498
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499
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500 def get(self, name):
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501 """Get an attribute value by name.
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502
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503 Given an attribute 'name' it will get its value.
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504 There's always the possibility of using the methods:
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505
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506 get_'name'()
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507
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508 which are defined for all the existing attributes.
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509 """
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510
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511 return self.obj_dict['attributes'].get(name, None)
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512
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513
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514 def get_attributes(self):
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515 """"""
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516
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517 return self.obj_dict['attributes']
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518
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519
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520 def set_sequence(self, seq):
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521
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522 self.obj_dict['sequence'] = seq
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523
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524
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525 def get_sequence(self):
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526
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527 return self.obj_dict['sequence']
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528
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529
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530 def create_attribute_methods(self, obj_attributes):
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531
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532 #for attr in self.obj_dict['attributes']:
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533 for attr in obj_attributes:
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534
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535 # Generate all the Setter methods.
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536 #
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537 self.__setattr__(
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538 'set_'+attr,
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539 lambda x, a=attr :
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540 self.obj_dict['attributes'].__setitem__(a, x) )
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541
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542 # Generate all the Getter methods.
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543 #
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544 self.__setattr__(
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545 'get_'+attr, lambda a=attr : self.__get_attribute__(a))
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546
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547
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548
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549 class Error(Exception):
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550 """General error handling class.
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551 """
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552 def __init__(self, value):
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553 self.value = value
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554 def __str__(self):
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555 return self.value
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556
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557
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558 class InvocationException(Exception):
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559 """Indicate problem while running any GraphViz executable.
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560 """
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561 def __init__(self, value):
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562 self.value = value
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563 def __str__(self):
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564 return self.value
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565
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566
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567
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568 class Node(Common):
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569 """A graph node.
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570
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571 This class represents a graph's node with all its attributes.
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572
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573 node(name, attribute=value, ...)
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574
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575 name: node's name
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576
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577 All the attributes defined in the Graphviz dot language should
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578 be supported.
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579 """
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580
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581 def __init__(self, name = '', obj_dict = None, **attrs):
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582
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583 #
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584 # Nodes will take attributes of
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585 # all other types because the defaults
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586 # for any GraphViz object are dealt with
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587 # as if they were Node definitions
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588 #
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589
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590 if obj_dict is not None:
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591
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592 self.obj_dict = obj_dict
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593
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594 else:
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595
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596 self.obj_dict = dict()
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597
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598 # Copy the attributes
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599 #
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600 self.obj_dict[ 'attributes' ] = dict( attrs )
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601 self.obj_dict[ 'type' ] = 'node'
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602 self.obj_dict[ 'parent_graph' ] = None
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603 self.obj_dict[ 'parent_node_list' ] = None
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604 self.obj_dict[ 'sequence' ] = None
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605
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606 # Remove the compass point
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607 #
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608 port = None
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609 if isinstance(name, str_type) and not name.startswith('"'):
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610 idx = name.find(':')
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611 if idx > 0 and idx+1 < len(name):
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612 name, port = name[:idx], name[idx:]
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613
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614 if isinstance(name, int):
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615 name = str(name)
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616
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617 self.obj_dict['name'] = quote_if_necessary(name)
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618 self.obj_dict['port'] = port
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619
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620 self.create_attribute_methods(NODE_ATTRIBUTES)
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621
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622 def __str__(self):
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623 return self.to_string()
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624
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625
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626 def set_name(self, node_name):
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627 """Set the node's name."""
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628
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629 self.obj_dict['name'] = node_name
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630
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631
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632 def get_name(self):
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633 """Get the node's name."""
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634
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635 return self.obj_dict['name']
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636
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637
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638 def get_port(self):
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639 """Get the node's port."""
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640
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641 return self.obj_dict['port']
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642
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643
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644 def add_style(self, style):
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645
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646 styles = self.obj_dict['attributes'].get('style', None)
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647 if not styles and style:
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648 styles = [ style ]
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649 else:
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650 styles = styles.split(',')
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651 styles.append( style )
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652
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653 self.obj_dict['attributes']['style'] = ','.join( styles )
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654
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655
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656 def to_string(self):
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657 """Return string representation of node in DOT language."""
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658
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659
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660 # RMF: special case defaults for node, edge and graph properties.
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661 #
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662 node = quote_if_necessary(self.obj_dict['name'])
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663
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664 node_attr = list()
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665
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666 for attr in sorted(self.obj_dict['attributes']):
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diff changeset
667 value = self.obj_dict['attributes'][attr]
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668 if value == '':
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669 value = '""'
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670 if value is not None:
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671 node_attr.append(
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672 '%s=%s' % (attr, quote_if_necessary(value) ) )
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673 else:
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674 node_attr.append( attr )
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675
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676
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677 # No point in having nodes setting any defaults if the don't set
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678 # any attributes...
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679 #
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680 if node in ('graph', 'node', 'edge') and len(node_attr) == 0:
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parents:
diff changeset
681 return ''
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682
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diff changeset
683 node_attr = ', '.join(node_attr)
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diff changeset
684
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685 if node_attr:
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diff changeset
686 node += ' [' + node_attr + ']'
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687
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parents:
diff changeset
688 return node + ';'
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689
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690
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diff changeset
691
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parents:
diff changeset
692 class Edge(Common):
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parents:
diff changeset
693 """A graph edge.
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diff changeset
694
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parents:
diff changeset
695 This class represents a graph's edge with all its attributes.
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parents:
diff changeset
696
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parents:
diff changeset
697 edge(src, dst, attribute=value, ...)
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parents:
diff changeset
698
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diff changeset
699 src: source node, subgraph or cluster
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parents:
diff changeset
700 dst: destination node, subgraph or cluster
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diff changeset
701
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diff changeset
702 `src` and `dst` can be specified as a `Node`, `Subgraph` or
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parents:
diff changeset
703 `Cluster` object, or as the name string of such a component.
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diff changeset
704
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diff changeset
705 All the attributes defined in the Graphviz dot language should
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parents:
diff changeset
706 be supported.
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diff changeset
707
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parents:
diff changeset
708 Attributes can be set through the dynamically generated methods:
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parents:
diff changeset
709
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diff changeset
710 set_[attribute name], i.e. set_label, set_fontname
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parents:
diff changeset
711
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diff changeset
712 or directly by using the instance's special dictionary:
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parents:
diff changeset
713
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parents:
diff changeset
714 Edge.obj_dict['attributes'][attribute name], i.e.
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parents:
diff changeset
715
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parents:
diff changeset
716 edge_instance.obj_dict['attributes']['label']
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parents:
diff changeset
717 edge_instance.obj_dict['attributes']['fontname']
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parents:
diff changeset
718
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parents:
diff changeset
719 """
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parents:
diff changeset
720
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diff changeset
721 def __init__(self, src='', dst='', obj_dict=None, **attrs):
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diff changeset
722 self.obj_dict = dict()
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parents:
diff changeset
723 if isinstance(src, (Node, Subgraph, Cluster)):
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parents:
diff changeset
724 src = src.get_name()
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parents:
diff changeset
725 if isinstance(dst, (Node, Subgraph, Cluster)):
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parents:
diff changeset
726 dst = dst.get_name()
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parents:
diff changeset
727 points = (quote_if_necessary(src),
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parents:
diff changeset
728 quote_if_necessary(dst))
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parents:
diff changeset
729 self.obj_dict['points'] = points
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parents:
diff changeset
730 if obj_dict is None:
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parents:
diff changeset
731 # Copy the attributes
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parents:
diff changeset
732 self.obj_dict[ 'attributes' ] = dict( attrs )
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parents:
diff changeset
733 self.obj_dict[ 'type' ] = 'edge'
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parents:
diff changeset
734 self.obj_dict[ 'parent_graph' ] = None
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parents:
diff changeset
735 self.obj_dict[ 'parent_edge_list' ] = None
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parents:
diff changeset
736 self.obj_dict[ 'sequence' ] = None
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parents:
diff changeset
737 else:
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diff changeset
738 self.obj_dict = obj_dict
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parents:
diff changeset
739 self.create_attribute_methods(EDGE_ATTRIBUTES)
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parents:
diff changeset
740
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parents:
diff changeset
741 def __str__(self):
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parents:
diff changeset
742 return self.to_string()
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diff changeset
743
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diff changeset
744
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parents:
diff changeset
745 def get_source(self):
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parents:
diff changeset
746 """Get the edges source node name."""
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parents:
diff changeset
747
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parents:
diff changeset
748 return self.obj_dict['points'][0]
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parents:
diff changeset
749
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diff changeset
750
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parents:
diff changeset
751 def get_destination(self):
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parents:
diff changeset
752 """Get the edge's destination node name."""
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parents:
diff changeset
753
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parents:
diff changeset
754 return self.obj_dict['points'][1]
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parents:
diff changeset
755
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diff changeset
756
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diff changeset
757 def __hash__(self):
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diff changeset
758
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parents:
diff changeset
759 return hash( hash(self.get_source()) +
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parents:
diff changeset
760 hash(self.get_destination()) )
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parents:
diff changeset
761
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parents:
diff changeset
762
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parents:
diff changeset
763 def __eq__(self, edge):
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parents:
diff changeset
764 """Compare two edges.
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parents:
diff changeset
765
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parents:
diff changeset
766 If the parent graph is directed, arcs linking
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parents:
diff changeset
767 node A to B are considered equal and A->B != B->A
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parents:
diff changeset
768
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parents:
diff changeset
769 If the parent graph is undirected, any edge
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parents:
diff changeset
770 connecting two nodes is equal to any other
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parents:
diff changeset
771 edge connecting the same nodes, A->B == B->A
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parents:
diff changeset
772 """
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parents:
diff changeset
773
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parents:
diff changeset
774 if not isinstance(edge, Edge):
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parents:
diff changeset
775 raise Error('Can not compare and '
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
776 'edge to a non-edge object.')
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shellac
parents:
diff changeset
777
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shellac
parents:
diff changeset
778 if self.get_parent_graph().get_top_graph_type() == 'graph':
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shellac
parents:
diff changeset
779
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
780 # If the graph is undirected, the edge has neither
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shellac
parents:
diff changeset
781 # source nor destination.
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shellac
parents:
diff changeset
782 #
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shellac
parents:
diff changeset
783 if ( ( self.get_source() == edge.get_source() and
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
784 self.get_destination() == edge.get_destination() ) or
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
785 ( edge.get_source() == self.get_destination() and
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shellac
parents:
diff changeset
786 edge.get_destination() == self.get_source() ) ):
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shellac
parents:
diff changeset
787 return True
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shellac
parents:
diff changeset
788
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shellac
parents:
diff changeset
789 else:
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shellac
parents:
diff changeset
790
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shellac
parents:
diff changeset
791 if (self.get_source()==edge.get_source() and
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shellac
parents:
diff changeset
792 self.get_destination()==edge.get_destination()):
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shellac
parents:
diff changeset
793 return True
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shellac
parents:
diff changeset
794
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shellac
parents:
diff changeset
795 return False
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shellac
parents:
diff changeset
796
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shellac
parents:
diff changeset
797 if not PY3:
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shellac
parents:
diff changeset
798 def __ne__(self, other):
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shellac
parents:
diff changeset
799 result = self.__eq__(other)
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shellac
parents:
diff changeset
800 if result is NotImplemented:
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shellac
parents:
diff changeset
801 return NotImplemented
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shellac
parents:
diff changeset
802 return not result
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shellac
parents:
diff changeset
803
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parents:
diff changeset
804 def parse_node_ref(self, node_str):
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shellac
parents:
diff changeset
805
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shellac
parents:
diff changeset
806 if not isinstance(node_str, str):
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shellac
parents:
diff changeset
807 return node_str
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shellac
parents:
diff changeset
808
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shellac
parents:
diff changeset
809 if node_str.startswith('"') and node_str.endswith('"'):
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shellac
parents:
diff changeset
810
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shellac
parents:
diff changeset
811 return node_str
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shellac
parents:
diff changeset
812
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shellac
parents:
diff changeset
813 node_port_idx = node_str.rfind(':')
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shellac
parents:
diff changeset
814
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shellac
parents:
diff changeset
815 if (node_port_idx>0 and node_str[0]=='"' and
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shellac
parents:
diff changeset
816 node_str[node_port_idx-1]=='"'):
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shellac
parents:
diff changeset
817
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shellac
parents:
diff changeset
818 return node_str
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shellac
parents:
diff changeset
819
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shellac
parents:
diff changeset
820 if node_port_idx>0:
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shellac
parents:
diff changeset
821
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shellac
parents:
diff changeset
822 a = node_str[:node_port_idx]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
823 b = node_str[node_port_idx+1:]
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shellac
parents:
diff changeset
824
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shellac
parents:
diff changeset
825 node = quote_if_necessary(a)
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shellac
parents:
diff changeset
826
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shellac
parents:
diff changeset
827 node += ':'+quote_if_necessary(b)
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shellac
parents:
diff changeset
828
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shellac
parents:
diff changeset
829 return node
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shellac
parents:
diff changeset
830
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shellac
parents:
diff changeset
831 return node_str
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shellac
parents:
diff changeset
832
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parents:
diff changeset
833
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parents:
diff changeset
834 def to_string(self):
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shellac
parents:
diff changeset
835 """Return string representation of edge in DOT language."""
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shellac
parents:
diff changeset
836
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shellac
parents:
diff changeset
837 src = self.parse_node_ref( self.get_source() )
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shellac
parents:
diff changeset
838 dst = self.parse_node_ref( self.get_destination() )
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shellac
parents:
diff changeset
839
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parents:
diff changeset
840 if isinstance(src, frozendict):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
841 edge = [ Subgraph(obj_dict=src).to_string() ]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
842 elif isinstance(src, int):
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shellac
parents:
diff changeset
843 edge = [ str(src) ]
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parents:
diff changeset
844 else:
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shellac
parents:
diff changeset
845 edge = [ src ]
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shellac
parents:
diff changeset
846
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shellac
parents:
diff changeset
847 if (self.get_parent_graph() and
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
848 self.get_parent_graph().get_top_graph_type() and
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
849 self.get_parent_graph().get_top_graph_type() == 'digraph' ):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
850
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
851 edge.append( '->' )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
852
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
853 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
854 edge.append( '--' )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
855
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
856 if isinstance(dst, frozendict):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
857 edge.append( Subgraph(obj_dict=dst).to_string() )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
858 elif isinstance(dst, int):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
859 edge.append( str(dst) )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
860 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
861 edge.append( dst )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
862
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
863
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
864 edge_attr = list()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
865
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shellac
parents:
diff changeset
866 for attr in sorted(self.obj_dict['attributes']):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
867 value = self.obj_dict['attributes'][attr]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
868 if value == '':
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
869 value = '""'
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
870 if value is not None:
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shellac
parents:
diff changeset
871 edge_attr.append(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
872 '%s=%s' % (attr, quote_if_necessary(value) ) )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
873 else:
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shellac
parents:
diff changeset
874 edge_attr.append( attr )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
875
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shellac
parents:
diff changeset
876 edge_attr = ', '.join(edge_attr)
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shellac
parents:
diff changeset
877
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
878 if edge_attr:
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shellac
parents:
diff changeset
879 edge.append( ' [' + edge_attr + ']' )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
880
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
881 return ' '.join(edge) + ';'
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
882
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
883
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
884
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
885
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
886
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
887 class Graph(Common):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
888 """Class representing a graph in Graphviz's dot language.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
889
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
890 This class implements the methods to work on a representation
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
891 of a graph in Graphviz's dot language.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
892
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
893 graph( graph_name='G', graph_type='digraph',
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
894 strict=False, suppress_disconnected=False, attribute=value, ...)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
895
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
896 graph_name:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
897 the graph's name
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
898 graph_type:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
899 can be 'graph' or 'digraph'
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
900 suppress_disconnected:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
901 defaults to False, which will remove from the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
902 graph any disconnected nodes.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
903 simplify:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
904 if True it will avoid displaying equal edges, i.e.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
905 only one edge between two nodes. removing the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
906 duplicated ones.
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parents:
diff changeset
907
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shellac
parents:
diff changeset
908 All the attributes defined in the Graphviz dot language should
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parents:
diff changeset
909 be supported.
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parents:
diff changeset
910
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parents:
diff changeset
911 Attributes can be set through the dynamically generated methods:
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shellac
parents:
diff changeset
912
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shellac
parents:
diff changeset
913 set_[attribute name], i.e. set_size, set_fontname
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shellac
parents:
diff changeset
914
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shellac
parents:
diff changeset
915 or using the instance's attributes:
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shellac
parents:
diff changeset
916
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shellac
parents:
diff changeset
917 Graph.obj_dict['attributes'][attribute name], i.e.
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shellac
parents:
diff changeset
918
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shellac
parents:
diff changeset
919 graph_instance.obj_dict['attributes']['label']
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shellac
parents:
diff changeset
920 graph_instance.obj_dict['attributes']['fontname']
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shellac
parents:
diff changeset
921 """
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parents:
diff changeset
922
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parents:
diff changeset
923
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parents:
diff changeset
924 def __init__(self, graph_name='G', obj_dict=None,
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shellac
parents:
diff changeset
925 graph_type='digraph', strict=False,
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parents:
diff changeset
926 suppress_disconnected=False, simplify=False, **attrs):
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shellac
parents:
diff changeset
927
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shellac
parents:
diff changeset
928 if obj_dict is not None:
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shellac
parents:
diff changeset
929 self.obj_dict = obj_dict
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shellac
parents:
diff changeset
930
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shellac
parents:
diff changeset
931 else:
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parents:
diff changeset
932
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parents:
diff changeset
933 self.obj_dict = dict()
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shellac
parents:
diff changeset
934
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parents:
diff changeset
935 self.obj_dict['attributes'] = dict(attrs)
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shellac
parents:
diff changeset
936
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shellac
parents:
diff changeset
937 if graph_type not in ['graph', 'digraph']:
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shellac
parents:
diff changeset
938 raise Error((
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shellac
parents:
diff changeset
939 'Invalid type "{t}". '
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shellac
parents:
diff changeset
940 'Accepted graph types are: '
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shellac
parents:
diff changeset
941 'graph, digraph').format(t=graph_type))
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shellac
parents:
diff changeset
942
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parents:
diff changeset
943
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parents:
diff changeset
944 self.obj_dict['name'] = quote_if_necessary(graph_name)
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shellac
parents:
diff changeset
945 self.obj_dict['type'] = graph_type
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parents:
diff changeset
946
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parents:
diff changeset
947 self.obj_dict['strict'] = strict
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shellac
parents:
diff changeset
948 self.obj_dict['suppress_disconnected'] = suppress_disconnected
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shellac
parents:
diff changeset
949 self.obj_dict['simplify'] = simplify
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shellac
parents:
diff changeset
950
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shellac
parents:
diff changeset
951 self.obj_dict['current_child_sequence'] = 1
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shellac
parents:
diff changeset
952 self.obj_dict['nodes'] = dict()
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shellac
parents:
diff changeset
953 self.obj_dict['edges'] = dict()
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shellac
parents:
diff changeset
954 self.obj_dict['subgraphs'] = dict()
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shellac
parents:
diff changeset
955
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shellac
parents:
diff changeset
956 self.set_parent_graph(self)
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shellac
parents:
diff changeset
957
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shellac
parents:
diff changeset
958
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shellac
parents:
diff changeset
959 self.create_attribute_methods(GRAPH_ATTRIBUTES)
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shellac
parents:
diff changeset
960
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shellac
parents:
diff changeset
961 def __str__(self):
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parents:
diff changeset
962 return self.to_string()
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parents:
diff changeset
963
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shellac
parents:
diff changeset
964
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parents:
diff changeset
965 def get_graph_type(self):
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shellac
parents:
diff changeset
966
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shellac
parents:
diff changeset
967 return self.obj_dict['type']
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shellac
parents:
diff changeset
968
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shellac
parents:
diff changeset
969
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parents:
diff changeset
970 def get_top_graph_type(self):
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shellac
parents:
diff changeset
971
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shellac
parents:
diff changeset
972 parent = self
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shellac
parents:
diff changeset
973 while True:
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shellac
parents:
diff changeset
974 parent_ = parent.get_parent_graph()
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shellac
parents:
diff changeset
975 if parent_ == parent:
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shellac
parents:
diff changeset
976 break
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shellac
parents:
diff changeset
977 parent = parent_
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parents:
diff changeset
978
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shellac
parents:
diff changeset
979 return parent.obj_dict['type']
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shellac
parents:
diff changeset
980
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shellac
parents:
diff changeset
981
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shellac
parents:
diff changeset
982 def set_graph_defaults(self, **attrs):
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shellac
parents:
diff changeset
983
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shellac
parents:
diff changeset
984 self.add_node( Node('graph', **attrs) )
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shellac
parents:
diff changeset
985
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shellac
parents:
diff changeset
986
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parents:
diff changeset
987 def get_graph_defaults(self, **attrs):
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shellac
parents:
diff changeset
988
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shellac
parents:
diff changeset
989 graph_nodes = self.get_node('graph')
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shellac
parents:
diff changeset
990
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parents:
diff changeset
991 if isinstance( graph_nodes, (list, tuple)):
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shellac
parents:
diff changeset
992 return [ node.get_attributes() for node in graph_nodes ]
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shellac
parents:
diff changeset
993
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shellac
parents:
diff changeset
994 return graph_nodes.get_attributes()
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shellac
parents:
diff changeset
995
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shellac
parents:
diff changeset
996
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shellac
parents:
diff changeset
997
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shellac
parents:
diff changeset
998 def set_node_defaults(self, **attrs):
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shellac
parents:
diff changeset
999 """Define default node attributes.
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shellac
parents:
diff changeset
1000
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shellac
parents:
diff changeset
1001 These attributes only apply to nodes added to the graph after
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shellac
parents:
diff changeset
1002 calling this method.
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shellac
parents:
diff changeset
1003 """
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shellac
parents:
diff changeset
1004 self.add_node( Node('node', **attrs) )
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shellac
parents:
diff changeset
1005
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shellac
parents:
diff changeset
1006
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shellac
parents:
diff changeset
1007 def get_node_defaults(self, **attrs):
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shellac
parents:
diff changeset
1008
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shellac
parents:
diff changeset
1009
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shellac
parents:
diff changeset
1010 graph_nodes = self.get_node('node')
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shellac
parents:
diff changeset
1011
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shellac
parents:
diff changeset
1012 if isinstance( graph_nodes, (list, tuple)):
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shellac
parents:
diff changeset
1013 return [ node.get_attributes() for node in graph_nodes ]
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shellac
parents:
diff changeset
1014
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shellac
parents:
diff changeset
1015 return graph_nodes.get_attributes()
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shellac
parents:
diff changeset
1016
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shellac
parents:
diff changeset
1017
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parents:
diff changeset
1018 def set_edge_defaults(self, **attrs):
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shellac
parents:
diff changeset
1019
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parents:
diff changeset
1020 self.add_node( Node('edge', **attrs) )
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shellac
parents:
diff changeset
1021
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shellac
parents:
diff changeset
1022
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shellac
parents:
diff changeset
1023
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parents:
diff changeset
1024 def get_edge_defaults(self, **attrs):
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shellac
parents:
diff changeset
1025
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parents:
diff changeset
1026 graph_nodes = self.get_node('edge')
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shellac
parents:
diff changeset
1027
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parents:
diff changeset
1028 if isinstance( graph_nodes, (list, tuple)):
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shellac
parents:
diff changeset
1029 return [ node.get_attributes() for node in graph_nodes ]
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shellac
parents:
diff changeset
1030
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shellac
parents:
diff changeset
1031 return graph_nodes.get_attributes()
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shellac
parents:
diff changeset
1032
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shellac
parents:
diff changeset
1033
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shellac
parents:
diff changeset
1034
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shellac
parents:
diff changeset
1035 def set_simplify(self, simplify):
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shellac
parents:
diff changeset
1036 """Set whether to simplify or not.
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shellac
parents:
diff changeset
1037
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shellac
parents:
diff changeset
1038 If True it will avoid displaying equal edges, i.e.
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shellac
parents:
diff changeset
1039 only one edge between two nodes. removing the
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shellac
parents:
diff changeset
1040 duplicated ones.
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shellac
parents:
diff changeset
1041 """
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shellac
parents:
diff changeset
1042
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parents:
diff changeset
1043 self.obj_dict['simplify'] = simplify
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shellac
parents:
diff changeset
1044
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shellac
parents:
diff changeset
1045
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shellac
parents:
diff changeset
1046
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parents:
diff changeset
1047 def get_simplify(self):
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shellac
parents:
diff changeset
1048 """Get whether to simplify or not.
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shellac
parents:
diff changeset
1049
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parents:
diff changeset
1050 Refer to set_simplify for more information.
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shellac
parents:
diff changeset
1051 """
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shellac
parents:
diff changeset
1052
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parents:
diff changeset
1053 return self.obj_dict['simplify']
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shellac
parents:
diff changeset
1054
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shellac
parents:
diff changeset
1055
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parents:
diff changeset
1056 def set_type(self, graph_type):
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shellac
parents:
diff changeset
1057 """Set the graph's type, 'graph' or 'digraph'."""
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shellac
parents:
diff changeset
1058
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parents:
diff changeset
1059 self.obj_dict['type'] = graph_type
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shellac
parents:
diff changeset
1060
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shellac
parents:
diff changeset
1061
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shellac
parents:
diff changeset
1062
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parents:
diff changeset
1063 def get_type(self):
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parents:
diff changeset
1064 """Get the graph's type, 'graph' or 'digraph'."""
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shellac
parents:
diff changeset
1065
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parents:
diff changeset
1066 return self.obj_dict['type']
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shellac
parents:
diff changeset
1067
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shellac
parents:
diff changeset
1068
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shellac
parents:
diff changeset
1069
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parents:
diff changeset
1070 def set_name(self, graph_name):
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shellac
parents:
diff changeset
1071 """Set the graph's name."""
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shellac
parents:
diff changeset
1072
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parents:
diff changeset
1073 self.obj_dict['name'] = graph_name
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shellac
parents:
diff changeset
1074
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shellac
parents:
diff changeset
1075
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shellac
parents:
diff changeset
1076
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parents:
diff changeset
1077 def get_name(self):
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parents:
diff changeset
1078 """Get the graph's name."""
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shellac
parents:
diff changeset
1079
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parents:
diff changeset
1080 return self.obj_dict['name']
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shellac
parents:
diff changeset
1081
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shellac
parents:
diff changeset
1082
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shellac
parents:
diff changeset
1083
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parents:
diff changeset
1084 def set_strict(self, val):
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shellac
parents:
diff changeset
1085 """Set graph to 'strict' mode.
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shellac
parents:
diff changeset
1086
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parents:
diff changeset
1087 This option is only valid for top level graphs.
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shellac
parents:
diff changeset
1088 """
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shellac
parents:
diff changeset
1089
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diff changeset
1090 self.obj_dict['strict'] = val
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shellac
parents:
diff changeset
1091
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shellac
parents:
diff changeset
1092
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parents:
diff changeset
1093
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parents:
diff changeset
1094 def get_strict(self, val):
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parents:
diff changeset
1095 """Get graph's 'strict' mode (True, False).
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shellac
parents:
diff changeset
1096
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parents:
diff changeset
1097 This option is only valid for top level graphs.
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shellac
parents:
diff changeset
1098 """
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shellac
parents:
diff changeset
1099
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parents:
diff changeset
1100 return self.obj_dict['strict']
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parents:
diff changeset
1101
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shellac
parents:
diff changeset
1102
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diff changeset
1103
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parents:
diff changeset
1104 def set_suppress_disconnected(self, val):
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parents:
diff changeset
1105 """Suppress disconnected nodes in the output graph.
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parents:
diff changeset
1106
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parents:
diff changeset
1107 This option will skip nodes in
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parents:
diff changeset
1108 the graph with no incoming or outgoing
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parents:
diff changeset
1109 edges. This option works also
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parents:
diff changeset
1110 for subgraphs and has effect only in the
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parents:
diff changeset
1111 current graph/subgraph.
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shellac
parents:
diff changeset
1112 """
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shellac
parents:
diff changeset
1113
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parents:
diff changeset
1114 self.obj_dict['suppress_disconnected'] = val
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shellac
parents:
diff changeset
1115
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shellac
parents:
diff changeset
1116
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parents:
diff changeset
1117
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parents:
diff changeset
1118 def get_suppress_disconnected(self, val):
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shellac
parents:
diff changeset
1119 """Get if suppress disconnected is set.
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shellac
parents:
diff changeset
1120
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shellac
parents:
diff changeset
1121 Refer to set_suppress_disconnected for more information.
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parents:
diff changeset
1122 """
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shellac
parents:
diff changeset
1123
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parents:
diff changeset
1124 return self.obj_dict['suppress_disconnected']
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shellac
parents:
diff changeset
1125
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parents:
diff changeset
1126
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parents:
diff changeset
1127 def get_next_sequence_number(self):
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parents:
diff changeset
1128
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parents:
diff changeset
1129 seq = self.obj_dict['current_child_sequence']
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parents:
diff changeset
1130
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shellac
parents:
diff changeset
1131 self.obj_dict['current_child_sequence'] += 1
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shellac
parents:
diff changeset
1132
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parents:
diff changeset
1133 return seq
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parents:
diff changeset
1134
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parents:
diff changeset
1135
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parents:
diff changeset
1136
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parents:
diff changeset
1137 def add_node(self, graph_node):
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shellac
parents:
diff changeset
1138 """Adds a node object to the graph.
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shellac
parents:
diff changeset
1139
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parents:
diff changeset
1140 It takes a node object as its only argument and returns
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parents:
diff changeset
1141 None.
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parents:
diff changeset
1142 """
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parents:
diff changeset
1143
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parents:
diff changeset
1144 if not isinstance(graph_node, Node):
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shellac
parents:
diff changeset
1145 raise TypeError(
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parents:
diff changeset
1146 'add_node() received ' +
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shellac
parents:
diff changeset
1147 'a non node class object: ' + str(graph_node))
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shellac
parents:
diff changeset
1148
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parents:
diff changeset
1149
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parents:
diff changeset
1150 node = self.get_node(graph_node.get_name())
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parents:
diff changeset
1151
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parents:
diff changeset
1152 if not node:
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parents:
diff changeset
1153
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parents:
diff changeset
1154 self.obj_dict['nodes'][graph_node.get_name()] = [
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parents:
diff changeset
1155 graph_node.obj_dict ]
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parents:
diff changeset
1156
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parents:
diff changeset
1157 #self.node_dict[graph_node.get_name()] = graph_node.attributes
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parents:
diff changeset
1158 graph_node.set_parent_graph(self.get_parent_graph())
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parents:
diff changeset
1159
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parents:
diff changeset
1160 else:
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parents:
diff changeset
1161
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parents:
diff changeset
1162 self.obj_dict['nodes'][graph_node.get_name()].append(
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parents:
diff changeset
1163 graph_node.obj_dict )
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parents:
diff changeset
1164
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parents:
diff changeset
1165 graph_node.set_sequence(self.get_next_sequence_number())
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parents:
diff changeset
1166
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shellac
parents:
diff changeset
1167
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parents:
diff changeset
1168
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parents:
diff changeset
1169 def del_node(self, name, index=None):
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parents:
diff changeset
1170 """Delete a node from the graph.
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parents:
diff changeset
1171
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parents:
diff changeset
1172 Given a node's name all node(s) with that same name
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parents:
diff changeset
1173 will be deleted if 'index' is not specified or set
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parents:
diff changeset
1174 to None.
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parents:
diff changeset
1175 If there are several nodes with that same name and
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parents:
diff changeset
1176 'index' is given, only the node in that position
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parents:
diff changeset
1177 will be deleted.
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parents:
diff changeset
1178
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diff changeset
1179 'index' should be an integer specifying the position
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parents:
diff changeset
1180 of the node to delete. If index is larger than the
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parents:
diff changeset
1181 number of nodes with that name, no action is taken.
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parents:
diff changeset
1182
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parents:
diff changeset
1183 If nodes are deleted it returns True. If no action
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parents:
diff changeset
1184 is taken it returns False.
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parents:
diff changeset
1185 """
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parents:
diff changeset
1186
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parents:
diff changeset
1187 if isinstance(name, Node):
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parents:
diff changeset
1188 name = name.get_name()
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parents:
diff changeset
1189
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diff changeset
1190 if name in self.obj_dict['nodes']:
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parents:
diff changeset
1191
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diff changeset
1192 if (index is not None and
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parents:
diff changeset
1193 index < len(self.obj_dict['nodes'][name])):
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parents:
diff changeset
1194 del self.obj_dict['nodes'][name][index]
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parents:
diff changeset
1195 return True
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parents:
diff changeset
1196 else:
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parents:
diff changeset
1197 del self.obj_dict['nodes'][name]
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parents:
diff changeset
1198 return True
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parents:
diff changeset
1199
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parents:
diff changeset
1200 return False
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parents:
diff changeset
1201
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parents:
diff changeset
1202
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parents:
diff changeset
1203 def get_node(self, name):
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parents:
diff changeset
1204 """Retrieve a node from the graph.
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shellac
parents:
diff changeset
1205
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parents:
diff changeset
1206 Given a node's name the corresponding Node
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shellac
parents:
diff changeset
1207 instance will be returned.
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parents:
diff changeset
1208
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parents:
diff changeset
1209 If one or more nodes exist with that name a list of
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shellac
parents:
diff changeset
1210 Node instances is returned.
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parents:
diff changeset
1211 An empty list is returned otherwise.
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parents:
diff changeset
1212 """
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shellac
parents:
diff changeset
1213
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parents:
diff changeset
1214 match = list()
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parents:
diff changeset
1215
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parents:
diff changeset
1216 if name in self.obj_dict['nodes']:
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parents:
diff changeset
1217
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parents:
diff changeset
1218 match.extend(
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parents:
diff changeset
1219 [Node(obj_dict=obj_dict)
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shellac
parents:
diff changeset
1220 for obj_dict in self.obj_dict['nodes'][name]])
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shellac
parents:
diff changeset
1221
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shellac
parents:
diff changeset
1222 return match
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shellac
parents:
diff changeset
1223
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shellac
parents:
diff changeset
1224
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parents:
diff changeset
1225 def get_nodes(self):
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parents:
diff changeset
1226 """Get the list of Node instances."""
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parents:
diff changeset
1227
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parents:
diff changeset
1228 return self.get_node_list()
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parents:
diff changeset
1229
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shellac
parents:
diff changeset
1230
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parents:
diff changeset
1231 def get_node_list(self):
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shellac
parents:
diff changeset
1232 """Get the list of Node instances.
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shellac
parents:
diff changeset
1233
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parents:
diff changeset
1234 This method returns the list of Node instances
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parents:
diff changeset
1235 composing the graph.
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parents:
diff changeset
1236 """
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parents:
diff changeset
1237
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parents:
diff changeset
1238 node_objs = list()
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parents:
diff changeset
1239
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parents:
diff changeset
1240 for node in self.obj_dict['nodes']:
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shellac
parents:
diff changeset
1241 obj_dict_list = self.obj_dict['nodes'][node]
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shellac
parents:
diff changeset
1242 node_objs.extend( [ Node( obj_dict = obj_d )
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shellac
parents:
diff changeset
1243 for obj_d in obj_dict_list ] )
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parents:
diff changeset
1244
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parents:
diff changeset
1245 return node_objs
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shellac
parents:
diff changeset
1246
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shellac
parents:
diff changeset
1247
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shellac
parents:
diff changeset
1248
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parents:
diff changeset
1249 def add_edge(self, graph_edge):
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shellac
parents:
diff changeset
1250 """Adds an edge object to the graph.
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shellac
parents:
diff changeset
1251
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shellac
parents:
diff changeset
1252 It takes a edge object as its only argument and returns
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shellac
parents:
diff changeset
1253 None.
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shellac
parents:
diff changeset
1254 """
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shellac
parents:
diff changeset
1255
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shellac
parents:
diff changeset
1256 if not isinstance(graph_edge, Edge):
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shellac
parents:
diff changeset
1257 raise TypeError(
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shellac
parents:
diff changeset
1258 'add_edge() received a non edge class object: ' +
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shellac
parents:
diff changeset
1259 str(graph_edge))
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parents:
diff changeset
1260
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shellac
parents:
diff changeset
1261 edge_points = ( graph_edge.get_source(),
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shellac
parents:
diff changeset
1262 graph_edge.get_destination() )
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parents:
diff changeset
1263
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parents:
diff changeset
1264 if edge_points in self.obj_dict['edges']:
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shellac
parents:
diff changeset
1265
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shellac
parents:
diff changeset
1266 edge_list = self.obj_dict['edges'][edge_points]
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shellac
parents:
diff changeset
1267 edge_list.append(graph_edge.obj_dict)
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shellac
parents:
diff changeset
1268
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parents:
diff changeset
1269 else:
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parents:
diff changeset
1270
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parents:
diff changeset
1271 self.obj_dict['edges'][edge_points] = [ graph_edge.obj_dict ]
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shellac
parents:
diff changeset
1272
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shellac
parents:
diff changeset
1273
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parents:
diff changeset
1274 graph_edge.set_sequence( self.get_next_sequence_number() )
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shellac
parents:
diff changeset
1275
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shellac
parents:
diff changeset
1276 graph_edge.set_parent_graph( self.get_parent_graph() )
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shellac
parents:
diff changeset
1277
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shellac
parents:
diff changeset
1278
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shellac
parents:
diff changeset
1279
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shellac
parents:
diff changeset
1280 def del_edge(self, src_or_list, dst=None, index=None):
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shellac
parents:
diff changeset
1281 """Delete an edge from the graph.
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shellac
parents:
diff changeset
1282
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shellac
parents:
diff changeset
1283 Given an edge's (source, destination) node names all
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shellac
parents:
diff changeset
1284 matching edges(s) will be deleted if 'index' is not
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shellac
parents:
diff changeset
1285 specified or set to None.
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shellac
parents:
diff changeset
1286 If there are several matching edges and 'index' is
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shellac
parents:
diff changeset
1287 given, only the edge in that position will be deleted.
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shellac
parents:
diff changeset
1288
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shellac
parents:
diff changeset
1289 'index' should be an integer specifying the position
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shellac
parents:
diff changeset
1290 of the edge to delete. If index is larger than the
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shellac
parents:
diff changeset
1291 number of matching edges, no action is taken.
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shellac
parents:
diff changeset
1292
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shellac
parents:
diff changeset
1293 If edges are deleted it returns True. If no action
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shellac
parents:
diff changeset
1294 is taken it returns False.
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shellac
parents:
diff changeset
1295 """
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shellac
parents:
diff changeset
1296
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shellac
parents:
diff changeset
1297 if isinstance( src_or_list, (list, tuple)):
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shellac
parents:
diff changeset
1298 if dst is not None and isinstance(dst, int):
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shellac
parents:
diff changeset
1299 index = dst
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shellac
parents:
diff changeset
1300 src, dst = src_or_list
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shellac
parents:
diff changeset
1301 else:
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shellac
parents:
diff changeset
1302 src, dst = src_or_list, dst
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shellac
parents:
diff changeset
1303
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shellac
parents:
diff changeset
1304 if isinstance(src, Node):
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shellac
parents:
diff changeset
1305 src = src.get_name()
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shellac
parents:
diff changeset
1306
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shellac
parents:
diff changeset
1307 if isinstance(dst, Node):
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shellac
parents:
diff changeset
1308 dst = dst.get_name()
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shellac
parents:
diff changeset
1309
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shellac
parents:
diff changeset
1310 if (src, dst) in self.obj_dict['edges']:
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shellac
parents:
diff changeset
1311
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shellac
parents:
diff changeset
1312 if (index is not None and
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shellac
parents:
diff changeset
1313 index < len(self.obj_dict['edges'][(src, dst)])):
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shellac
parents:
diff changeset
1314 del self.obj_dict['edges'][(src, dst)][index]
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shellac
parents:
diff changeset
1315 return True
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shellac
parents:
diff changeset
1316 else:
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shellac
parents:
diff changeset
1317 del self.obj_dict['edges'][(src, dst)]
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shellac
parents:
diff changeset
1318 return True
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shellac
parents:
diff changeset
1319
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shellac
parents:
diff changeset
1320 return False
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shellac
parents:
diff changeset
1321
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shellac
parents:
diff changeset
1322
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shellac
parents:
diff changeset
1323 def get_edge(self, src_or_list, dst=None):
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shellac
parents:
diff changeset
1324 """Retrieved an edge from the graph.
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shellac
parents:
diff changeset
1325
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shellac
parents:
diff changeset
1326 Given an edge's source and destination the corresponding
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1327 Edge instance(s) will be returned.
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shellac
parents:
diff changeset
1328
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shellac
parents:
diff changeset
1329 If one or more edges exist with that source and destination
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shellac
parents:
diff changeset
1330 a list of Edge instances is returned.
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shellac
parents:
diff changeset
1331 An empty list is returned otherwise.
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shellac
parents:
diff changeset
1332 """
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shellac
parents:
diff changeset
1333
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shellac
parents:
diff changeset
1334 if isinstance( src_or_list, (list, tuple)) and dst is None:
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shellac
parents:
diff changeset
1335 edge_points = tuple(src_or_list)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1336 edge_points_reverse = (edge_points[1], edge_points[0])
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shellac
parents:
diff changeset
1337 else:
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shellac
parents:
diff changeset
1338 edge_points = (src_or_list, dst)
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shellac
parents:
diff changeset
1339 edge_points_reverse = (dst, src_or_list)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1340
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shellac
parents:
diff changeset
1341 match = list()
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shellac
parents:
diff changeset
1342
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shellac
parents:
diff changeset
1343 if edge_points in self.obj_dict['edges'] or (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1344 self.get_top_graph_type() == 'graph' and
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1345 edge_points_reverse in self.obj_dict['edges']):
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shellac
parents:
diff changeset
1346
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shellac
parents:
diff changeset
1347 edges_obj_dict = self.obj_dict['edges'].get(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1348 edge_points,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1349 self.obj_dict['edges'].get( edge_points_reverse, None ))
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shellac
parents:
diff changeset
1350
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shellac
parents:
diff changeset
1351 for edge_obj_dict in edges_obj_dict:
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shellac
parents:
diff changeset
1352 match.append(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1353 Edge(edge_points[0],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1354 edge_points[1],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1355 obj_dict=edge_obj_dict))
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shellac
parents:
diff changeset
1356
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shellac
parents:
diff changeset
1357 return match
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shellac
parents:
diff changeset
1358
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shellac
parents:
diff changeset
1359
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shellac
parents:
diff changeset
1360 def get_edges(self):
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shellac
parents:
diff changeset
1361 return self.get_edge_list()
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shellac
parents:
diff changeset
1362
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shellac
parents:
diff changeset
1363
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shellac
parents:
diff changeset
1364 def get_edge_list(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1365 """Get the list of Edge instances.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1366
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shellac
parents:
diff changeset
1367 This method returns the list of Edge instances
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1368 composing the graph.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1369 """
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shellac
parents:
diff changeset
1370
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shellac
parents:
diff changeset
1371 edge_objs = list()
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shellac
parents:
diff changeset
1372
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shellac
parents:
diff changeset
1373 for edge in self.obj_dict['edges']:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1374 obj_dict_list = self.obj_dict['edges'][edge]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1375 edge_objs.extend(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1376 [Edge(obj_dict=obj_d)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1377 for obj_d in obj_dict_list])
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shellac
parents:
diff changeset
1378
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shellac
parents:
diff changeset
1379 return edge_objs
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shellac
parents:
diff changeset
1380
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1381
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shellac
parents:
diff changeset
1382
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1383 def add_subgraph(self, sgraph):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1384 """Adds an subgraph object to the graph.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1385
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shellac
parents:
diff changeset
1386 It takes a subgraph object as its only argument and returns
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1387 None.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1388 """
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shellac
parents:
diff changeset
1389
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shellac
parents:
diff changeset
1390 if (not isinstance(sgraph, Subgraph) and
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1391 not isinstance(sgraph, Cluster)):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1392 raise TypeError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1393 'add_subgraph() received a non subgraph class object:' +
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1394 str(sgraph))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1395
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1396 if sgraph.get_name() in self.obj_dict['subgraphs']:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1397
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shellac
parents:
diff changeset
1398 sgraph_list = self.obj_dict['subgraphs'][ sgraph.get_name() ]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1399 sgraph_list.append( sgraph.obj_dict )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1400
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1401 else:
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shellac
parents:
diff changeset
1402 self.obj_dict['subgraphs'][sgraph.get_name()] = [
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1403 sgraph.obj_dict]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1404
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shellac
parents:
diff changeset
1405 sgraph.set_sequence( self.get_next_sequence_number() )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1406
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1407 sgraph.set_parent_graph( self.get_parent_graph() )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1408
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1409
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1410
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1411
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1412 def get_subgraph(self, name):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1413 """Retrieved a subgraph from the graph.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1414
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1415 Given a subgraph's name the corresponding
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1416 Subgraph instance will be returned.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1417
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shellac
parents:
diff changeset
1418 If one or more subgraphs exist with the same name, a list of
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1419 Subgraph instances is returned.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1420 An empty list is returned otherwise.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1421 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1422
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1423 match = list()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1424
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1425 if name in self.obj_dict['subgraphs']:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1426
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shellac
parents:
diff changeset
1427 sgraphs_obj_dict = self.obj_dict['subgraphs'].get( name )
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shellac
parents:
diff changeset
1428
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shellac
parents:
diff changeset
1429 for obj_dict_list in sgraphs_obj_dict:
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shellac
parents:
diff changeset
1430 #match.extend( Subgraph( obj_dict = obj_d )
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shellac
parents:
diff changeset
1431 # for obj_d in obj_dict_list )
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shellac
parents:
diff changeset
1432 match.append( Subgraph( obj_dict = obj_dict_list ) )
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shellac
parents:
diff changeset
1433
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shellac
parents:
diff changeset
1434 return match
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parents:
diff changeset
1435
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parents:
diff changeset
1436
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shellac
parents:
diff changeset
1437 def get_subgraphs(self):
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shellac
parents:
diff changeset
1438
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shellac
parents:
diff changeset
1439 return self.get_subgraph_list()
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shellac
parents:
diff changeset
1440
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shellac
parents:
diff changeset
1441
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shellac
parents:
diff changeset
1442 def get_subgraph_list(self):
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shellac
parents:
diff changeset
1443 """Get the list of Subgraph instances.
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shellac
parents:
diff changeset
1444
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shellac
parents:
diff changeset
1445 This method returns the list of Subgraph instances
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shellac
parents:
diff changeset
1446 in the graph.
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shellac
parents:
diff changeset
1447 """
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shellac
parents:
diff changeset
1448
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shellac
parents:
diff changeset
1449 sgraph_objs = list()
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shellac
parents:
diff changeset
1450
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parents:
diff changeset
1451 for sgraph in self.obj_dict['subgraphs']:
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shellac
parents:
diff changeset
1452 obj_dict_list = self.obj_dict['subgraphs'][sgraph]
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shellac
parents:
diff changeset
1453 sgraph_objs.extend(
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shellac
parents:
diff changeset
1454 [Subgraph(obj_dict=obj_d)
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shellac
parents:
diff changeset
1455 for obj_d in obj_dict_list])
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shellac
parents:
diff changeset
1456
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shellac
parents:
diff changeset
1457 return sgraph_objs
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shellac
parents:
diff changeset
1458
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shellac
parents:
diff changeset
1459
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shellac
parents:
diff changeset
1460
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shellac
parents:
diff changeset
1461 def set_parent_graph(self, parent_graph):
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shellac
parents:
diff changeset
1462
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shellac
parents:
diff changeset
1463 self.obj_dict['parent_graph'] = parent_graph
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shellac
parents:
diff changeset
1464
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shellac
parents:
diff changeset
1465 for k in self.obj_dict['nodes']:
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shellac
parents:
diff changeset
1466 obj_list = self.obj_dict['nodes'][k]
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shellac
parents:
diff changeset
1467 for obj in obj_list:
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shellac
parents:
diff changeset
1468 obj['parent_graph'] = parent_graph
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shellac
parents:
diff changeset
1469
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shellac
parents:
diff changeset
1470 for k in self.obj_dict['edges']:
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shellac
parents:
diff changeset
1471 obj_list = self.obj_dict['edges'][k]
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shellac
parents:
diff changeset
1472 for obj in obj_list:
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shellac
parents:
diff changeset
1473 obj['parent_graph'] = parent_graph
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shellac
parents:
diff changeset
1474
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shellac
parents:
diff changeset
1475 for k in self.obj_dict['subgraphs']:
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shellac
parents:
diff changeset
1476 obj_list = self.obj_dict['subgraphs'][k]
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shellac
parents:
diff changeset
1477 for obj in obj_list:
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shellac
parents:
diff changeset
1478 Graph(obj_dict=obj).set_parent_graph(parent_graph)
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shellac
parents:
diff changeset
1479
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shellac
parents:
diff changeset
1480
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shellac
parents:
diff changeset
1481
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shellac
parents:
diff changeset
1482 def to_string(self):
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shellac
parents:
diff changeset
1483 """Return string representation of graph in DOT language.
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shellac
parents:
diff changeset
1484
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shellac
parents:
diff changeset
1485 @return: graph and subelements
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shellac
parents:
diff changeset
1486 @rtype: `str`
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shellac
parents:
diff changeset
1487 """
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shellac
parents:
diff changeset
1488
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shellac
parents:
diff changeset
1489
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shellac
parents:
diff changeset
1490 graph = list()
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parents:
diff changeset
1491
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shellac
parents:
diff changeset
1492 if self.obj_dict.get('strict', None) is not None:
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shellac
parents:
diff changeset
1493
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shellac
parents:
diff changeset
1494 if (self == self.get_parent_graph() and
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shellac
parents:
diff changeset
1495 self.obj_dict['strict']):
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shellac
parents:
diff changeset
1496
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shellac
parents:
diff changeset
1497 graph.append('strict ')
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shellac
parents:
diff changeset
1498
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shellac
parents:
diff changeset
1499 graph_type = self.obj_dict['type']
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shellac
parents:
diff changeset
1500 if (graph_type == 'subgraph' and
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shellac
parents:
diff changeset
1501 not self.obj_dict.get('show_keyword', True)):
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shellac
parents:
diff changeset
1502 graph_type = ''
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shellac
parents:
diff changeset
1503 s = '{type} {name} {{\n'.format(
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shellac
parents:
diff changeset
1504 type=graph_type,
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shellac
parents:
diff changeset
1505 name=self.obj_dict['name'])
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shellac
parents:
diff changeset
1506 graph.append(s)
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shellac
parents:
diff changeset
1507
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shellac
parents:
diff changeset
1508 for attr in sorted(self.obj_dict['attributes']):
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shellac
parents:
diff changeset
1509
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shellac
parents:
diff changeset
1510 if self.obj_dict['attributes'].get(attr, None) is not None:
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shellac
parents:
diff changeset
1511
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shellac
parents:
diff changeset
1512 val = self.obj_dict['attributes'].get(attr)
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shellac
parents:
diff changeset
1513 if val == '':
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shellac
parents:
diff changeset
1514 val = '""'
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shellac
parents:
diff changeset
1515 if val is not None:
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shellac
parents:
diff changeset
1516 graph.append('%s=%s' %
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1517 (attr, quote_if_necessary(val)))
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shellac
parents:
diff changeset
1518 else:
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shellac
parents:
diff changeset
1519 graph.append( attr )
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shellac
parents:
diff changeset
1520
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shellac
parents:
diff changeset
1521 graph.append( ';\n' )
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shellac
parents:
diff changeset
1522
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shellac
parents:
diff changeset
1523
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shellac
parents:
diff changeset
1524 edges_done = set()
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shellac
parents:
diff changeset
1525
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shellac
parents:
diff changeset
1526 edge_obj_dicts = list()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1527 for k in self.obj_dict['edges']:
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shellac
parents:
diff changeset
1528 edge_obj_dicts.extend(self.obj_dict['edges'][k])
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shellac
parents:
diff changeset
1529
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shellac
parents:
diff changeset
1530 if edge_obj_dicts:
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shellac
parents:
diff changeset
1531 edge_src_set, edge_dst_set = list(zip(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1532 *[obj['points'] for obj in edge_obj_dicts]))
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shellac
parents:
diff changeset
1533 edge_src_set, edge_dst_set = set(edge_src_set), set(edge_dst_set)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1534 else:
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shellac
parents:
diff changeset
1535 edge_src_set, edge_dst_set = set(), set()
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shellac
parents:
diff changeset
1536
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shellac
parents:
diff changeset
1537 node_obj_dicts = list()
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shellac
parents:
diff changeset
1538 for k in self.obj_dict['nodes']:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1539 node_obj_dicts.extend(self.obj_dict['nodes'][k])
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shellac
parents:
diff changeset
1540
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shellac
parents:
diff changeset
1541 sgraph_obj_dicts = list()
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shellac
parents:
diff changeset
1542 for k in self.obj_dict['subgraphs']:
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shellac
parents:
diff changeset
1543 sgraph_obj_dicts.extend(self.obj_dict['subgraphs'][k])
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shellac
parents:
diff changeset
1544
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shellac
parents:
diff changeset
1545
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shellac
parents:
diff changeset
1546 obj_list = [(obj['sequence'], obj)
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shellac
parents:
diff changeset
1547 for obj in (edge_obj_dicts +
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1548 node_obj_dicts + sgraph_obj_dicts) ]
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shellac
parents:
diff changeset
1549 obj_list.sort(key=lambda x: x[0])
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shellac
parents:
diff changeset
1550
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shellac
parents:
diff changeset
1551 for idx, obj in obj_list:
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shellac
parents:
diff changeset
1552
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shellac
parents:
diff changeset
1553 if obj['type'] == 'node':
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shellac
parents:
diff changeset
1554
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parents:
diff changeset
1555 node = Node(obj_dict=obj)
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parents:
diff changeset
1556
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parents:
diff changeset
1557 if self.obj_dict.get('suppress_disconnected', False):
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parents:
diff changeset
1558
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parents:
diff changeset
1559 if (node.get_name() not in edge_src_set and
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shellac
parents:
diff changeset
1560 node.get_name() not in edge_dst_set):
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shellac
parents:
diff changeset
1561
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parents:
diff changeset
1562 continue
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parents:
diff changeset
1563
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parents:
diff changeset
1564 graph.append( node.to_string()+'\n' )
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shellac
parents:
diff changeset
1565
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parents:
diff changeset
1566 elif obj['type'] == 'edge':
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parents:
diff changeset
1567
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parents:
diff changeset
1568 edge = Edge(obj_dict=obj)
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parents:
diff changeset
1569
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parents:
diff changeset
1570 if (self.obj_dict.get('simplify', False) and
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shellac
parents:
diff changeset
1571 edge in edges_done):
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parents:
diff changeset
1572 continue
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parents:
diff changeset
1573
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parents:
diff changeset
1574 graph.append( edge.to_string() + '\n' )
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shellac
parents:
diff changeset
1575 edges_done.add(edge)
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shellac
parents:
diff changeset
1576
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parents:
diff changeset
1577 else:
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parents:
diff changeset
1578
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parents:
diff changeset
1579 sgraph = Subgraph(obj_dict=obj)
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parents:
diff changeset
1580
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parents:
diff changeset
1581 graph.append( sgraph.to_string()+'\n' )
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parents:
diff changeset
1582
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parents:
diff changeset
1583 graph.append( '}\n' )
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parents:
diff changeset
1584
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parents:
diff changeset
1585 return ''.join(graph)
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parents:
diff changeset
1586
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parents:
diff changeset
1587
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parents:
diff changeset
1588
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parents:
diff changeset
1589 class Subgraph(Graph):
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parents:
diff changeset
1590
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parents:
diff changeset
1591 """Class representing a subgraph in Graphviz's dot language.
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parents:
diff changeset
1592
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parents:
diff changeset
1593 This class implements the methods to work on a representation
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parents:
diff changeset
1594 of a subgraph in Graphviz's dot language.
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parents:
diff changeset
1595
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parents:
diff changeset
1596 subgraph(graph_name='subG',
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parents:
diff changeset
1597 suppress_disconnected=False,
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parents:
diff changeset
1598 attribute=value,
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parents:
diff changeset
1599 ...)
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parents:
diff changeset
1600
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parents:
diff changeset
1601 graph_name:
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parents:
diff changeset
1602 the subgraph's name
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parents:
diff changeset
1603 suppress_disconnected:
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parents:
diff changeset
1604 defaults to false, which will remove from the
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parents:
diff changeset
1605 subgraph any disconnected nodes.
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parents:
diff changeset
1606 All the attributes defined in the Graphviz dot language should
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parents:
diff changeset
1607 be supported.
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parents:
diff changeset
1608
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parents:
diff changeset
1609 Attributes can be set through the dynamically generated methods:
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parents:
diff changeset
1610
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parents:
diff changeset
1611 set_[attribute name], i.e. set_size, set_fontname
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parents:
diff changeset
1612
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parents:
diff changeset
1613 or using the instance's attributes:
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parents:
diff changeset
1614
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parents:
diff changeset
1615 Subgraph.obj_dict['attributes'][attribute name], i.e.
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shellac
parents:
diff changeset
1616
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parents:
diff changeset
1617 subgraph_instance.obj_dict['attributes']['label']
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shellac
parents:
diff changeset
1618 subgraph_instance.obj_dict['attributes']['fontname']
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shellac
parents:
diff changeset
1619 """
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shellac
parents:
diff changeset
1620
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parents:
diff changeset
1621
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parents:
diff changeset
1622 # RMF: subgraph should have all the
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shellac
parents:
diff changeset
1623 # attributes of graph so it can be passed
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shellac
parents:
diff changeset
1624 # as a graph to all methods
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shellac
parents:
diff changeset
1625 #
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parents:
diff changeset
1626 def __init__(self, graph_name='',
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shellac
parents:
diff changeset
1627 obj_dict=None, suppress_disconnected=False,
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shellac
parents:
diff changeset
1628 simplify=False, **attrs):
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shellac
parents:
diff changeset
1629
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parents:
diff changeset
1630
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parents:
diff changeset
1631 Graph.__init__(
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parents:
diff changeset
1632 self, graph_name=graph_name, obj_dict=obj_dict,
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shellac
parents:
diff changeset
1633 suppress_disconnected=suppress_disconnected,
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shellac
parents:
diff changeset
1634 simplify=simplify, **attrs)
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shellac
parents:
diff changeset
1635
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parents:
diff changeset
1636 if obj_dict is None:
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shellac
parents:
diff changeset
1637
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parents:
diff changeset
1638 self.obj_dict['type'] = 'subgraph'
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shellac
parents:
diff changeset
1639
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shellac
parents:
diff changeset
1640
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shellac
parents:
diff changeset
1641
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shellac
parents:
diff changeset
1642
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shellac
parents:
diff changeset
1643 class Cluster(Graph):
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shellac
parents:
diff changeset
1644
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shellac
parents:
diff changeset
1645 """Class representing a cluster in Graphviz's dot language.
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shellac
parents:
diff changeset
1646
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shellac
parents:
diff changeset
1647 This class implements the methods to work on a representation
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shellac
parents:
diff changeset
1648 of a cluster in Graphviz's dot language.
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shellac
parents:
diff changeset
1649
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shellac
parents:
diff changeset
1650 cluster(graph_name='subG',
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shellac
parents:
diff changeset
1651 suppress_disconnected=False,
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shellac
parents:
diff changeset
1652 attribute=value,
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shellac
parents:
diff changeset
1653 ...)
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shellac
parents:
diff changeset
1654
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shellac
parents:
diff changeset
1655 graph_name:
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shellac
parents:
diff changeset
1656 the cluster's name
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shellac
parents:
diff changeset
1657 (the string 'cluster' will be always prepended)
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shellac
parents:
diff changeset
1658 suppress_disconnected:
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shellac
parents:
diff changeset
1659 defaults to false, which will remove from the
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shellac
parents:
diff changeset
1660 cluster any disconnected nodes.
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shellac
parents:
diff changeset
1661 All the attributes defined in the Graphviz dot language should
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1662 be supported.
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shellac
parents:
diff changeset
1663
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shellac
parents:
diff changeset
1664 Attributes can be set through the dynamically generated methods:
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shellac
parents:
diff changeset
1665
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shellac
parents:
diff changeset
1666 set_[attribute name], i.e. set_color, set_fontname
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shellac
parents:
diff changeset
1667
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shellac
parents:
diff changeset
1668 or using the instance's attributes:
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shellac
parents:
diff changeset
1669
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shellac
parents:
diff changeset
1670 Cluster.obj_dict['attributes'][attribute name], i.e.
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shellac
parents:
diff changeset
1671
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shellac
parents:
diff changeset
1672 cluster_instance.obj_dict['attributes']['label']
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shellac
parents:
diff changeset
1673 cluster_instance.obj_dict['attributes']['fontname']
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shellac
parents:
diff changeset
1674 """
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shellac
parents:
diff changeset
1675
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shellac
parents:
diff changeset
1676
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parents:
diff changeset
1677 def __init__(self, graph_name='subG',
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shellac
parents:
diff changeset
1678 obj_dict=None, suppress_disconnected=False,
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shellac
parents:
diff changeset
1679 simplify=False, **attrs):
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shellac
parents:
diff changeset
1680
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shellac
parents:
diff changeset
1681 Graph.__init__(
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shellac
parents:
diff changeset
1682 self, graph_name=graph_name, obj_dict=obj_dict,
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shellac
parents:
diff changeset
1683 suppress_disconnected=suppress_disconnected,
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shellac
parents:
diff changeset
1684 simplify=simplify, **attrs)
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diff changeset
1685
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diff changeset
1686 if obj_dict is None:
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parents:
diff changeset
1687
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parents:
diff changeset
1688 self.obj_dict['type'] = 'subgraph'
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parents:
diff changeset
1689 self.obj_dict['name'] = quote_if_necessary('cluster_'+graph_name)
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parents:
diff changeset
1690
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parents:
diff changeset
1691 self.create_attribute_methods(CLUSTER_ATTRIBUTES)
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parents:
diff changeset
1692
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parents:
diff changeset
1693
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parents:
diff changeset
1694
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parents:
diff changeset
1695
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parents:
diff changeset
1696
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parents:
diff changeset
1697
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parents:
diff changeset
1698 class Dot(Graph):
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parents:
diff changeset
1699 """A container for handling a dot language file.
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parents:
diff changeset
1700
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parents:
diff changeset
1701 This class implements methods to write and process
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shellac
parents:
diff changeset
1702 a dot language file. It is a derived class of
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parents:
diff changeset
1703 the base class 'Graph'.
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parents:
diff changeset
1704 """
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parents:
diff changeset
1705
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parents:
diff changeset
1706
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parents:
diff changeset
1707
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parents:
diff changeset
1708 def __init__(self, *argsl, **argsd):
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shellac
parents:
diff changeset
1709 Graph.__init__(self, *argsl, **argsd)
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parents:
diff changeset
1710
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parents:
diff changeset
1711 self.shape_files = list()
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parents:
diff changeset
1712 self.formats = [
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parents:
diff changeset
1713 'canon', 'cmap', 'cmapx',
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shellac
parents:
diff changeset
1714 'cmapx_np', 'dia', 'dot',
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shellac
parents:
diff changeset
1715 'fig', 'gd', 'gd2', 'gif',
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parents:
diff changeset
1716 'hpgl', 'imap', 'imap_np', 'ismap',
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parents:
diff changeset
1717 'jpe', 'jpeg', 'jpg', 'mif',
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parents:
diff changeset
1718 'mp', 'pcl', 'pdf', 'pic', 'plain',
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shellac
parents:
diff changeset
1719 'plain-ext', 'png', 'ps', 'ps2',
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shellac
parents:
diff changeset
1720 'svg', 'svgz', 'vml', 'vmlz',
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shellac
parents:
diff changeset
1721 'vrml', 'vtx', 'wbmp', 'xdot', 'xlib']
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parents:
diff changeset
1722
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parents:
diff changeset
1723 self.prog = 'dot'
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parents:
diff changeset
1724
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diff changeset
1725 # Automatically creates all
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parents:
diff changeset
1726 # the methods enabling the creation
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parents:
diff changeset
1727 # of output in any of the supported formats.
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shellac
parents:
diff changeset
1728 for frmt in self.formats:
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parents:
diff changeset
1729 def new_method(
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parents:
diff changeset
1730 f=frmt, prog=self.prog,
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parents:
diff changeset
1731 encoding=None):
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parents:
diff changeset
1732 """Refer to docstring of method `create`."""
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parents:
diff changeset
1733 return self.create(
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parents:
diff changeset
1734 format=f, prog=prog, encoding=encoding)
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shellac
parents:
diff changeset
1735 name = 'create_{fmt}'.format(fmt=frmt)
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shellac
parents:
diff changeset
1736 self.__setattr__(name, new_method)
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parents:
diff changeset
1737
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parents:
diff changeset
1738 for frmt in self.formats+['raw']:
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parents:
diff changeset
1739 def new_method(
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parents:
diff changeset
1740 path, f=frmt, prog=self.prog,
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parents:
diff changeset
1741 encoding=None):
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parents:
diff changeset
1742 """Refer to docstring of method `write.`"""
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parents:
diff changeset
1743 self.write(
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parents:
diff changeset
1744 path, format=f, prog=prog,
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parents:
diff changeset
1745 encoding=encoding)
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parents:
diff changeset
1746 name = 'write_{fmt}'.format(fmt=frmt)
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shellac
parents:
diff changeset
1747 self.__setattr__(name, new_method)
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parents:
diff changeset
1748
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parents:
diff changeset
1749 def __getstate__(self):
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parents:
diff changeset
1750
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parents:
diff changeset
1751 dict = copy.copy(self.obj_dict)
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parents:
diff changeset
1752
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parents:
diff changeset
1753 return dict
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parents:
diff changeset
1754
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parents:
diff changeset
1755 def __setstate__(self, state):
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parents:
diff changeset
1756
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parents:
diff changeset
1757 self.obj_dict = state
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parents:
diff changeset
1758
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parents:
diff changeset
1759
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shellac
parents:
diff changeset
1760 def set_shape_files(self, file_paths):
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shellac
parents:
diff changeset
1761 """Add the paths of the required image files.
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shellac
parents:
diff changeset
1762
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parents:
diff changeset
1763 If the graph needs graphic objects to
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parents:
diff changeset
1764 be used as shapes or otherwise
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shellac
parents:
diff changeset
1765 those need to be in the same folder as
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shellac
parents:
diff changeset
1766 the graph is going to be rendered
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shellac
parents:
diff changeset
1767 from. Alternatively the absolute path to
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shellac
parents:
diff changeset
1768 the files can be specified when
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shellac
parents:
diff changeset
1769 including the graphics in the graph.
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shellac
parents:
diff changeset
1770
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shellac
parents:
diff changeset
1771 The files in the location pointed to by
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shellac
parents:
diff changeset
1772 the path(s) specified as arguments
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shellac
parents:
diff changeset
1773 to this method will be copied to
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shellac
parents:
diff changeset
1774 the same temporary location where the
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parents:
diff changeset
1775 graph is going to be rendered.
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shellac
parents:
diff changeset
1776 """
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shellac
parents:
diff changeset
1777
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shellac
parents:
diff changeset
1778 if isinstance( file_paths, str_type):
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shellac
parents:
diff changeset
1779 self.shape_files.append( file_paths )
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parents:
diff changeset
1780
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parents:
diff changeset
1781 if isinstance( file_paths, (list, tuple) ):
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shellac
parents:
diff changeset
1782 self.shape_files.extend( file_paths )
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shellac
parents:
diff changeset
1783
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parents:
diff changeset
1784
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parents:
diff changeset
1785 def set_prog(self, prog):
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shellac
parents:
diff changeset
1786 """Sets the default program.
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shellac
parents:
diff changeset
1787
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parents:
diff changeset
1788 Sets the default program in charge of processing
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shellac
parents:
diff changeset
1789 the dot file into a graph.
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shellac
parents:
diff changeset
1790 """
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shellac
parents:
diff changeset
1791 self.prog = prog
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parents:
diff changeset
1792
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parents:
diff changeset
1793
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parents:
diff changeset
1794 def write(self, path, prog=None, format='raw', encoding=None):
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shellac
parents:
diff changeset
1795 """Writes a graph to a file.
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shellac
parents:
diff changeset
1796
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parents:
diff changeset
1797 Given a filename 'path' it will open/create and truncate
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shellac
parents:
diff changeset
1798 such file and write on it a representation of the graph
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shellac
parents:
diff changeset
1799 defined by the dot object in the format specified by
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shellac
parents:
diff changeset
1800 'format' and using the encoding specified by `encoding` for text.
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shellac
parents:
diff changeset
1801 The format 'raw' is used to dump the string representation
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shellac
parents:
diff changeset
1802 of the Dot object, without further processing.
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shellac
parents:
diff changeset
1803 The output can be processed by any of graphviz tools, defined
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shellac
parents:
diff changeset
1804 in 'prog', which defaults to 'dot'
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shellac
parents:
diff changeset
1805 Returns True or False according to the success of the write
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shellac
parents:
diff changeset
1806 operation.
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shellac
parents:
diff changeset
1807
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parents:
diff changeset
1808 There's also the preferred possibility of using:
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parents:
diff changeset
1809
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shellac
parents:
diff changeset
1810 write_'format'(path, prog='program')
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shellac
parents:
diff changeset
1811
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parents:
diff changeset
1812 which are automatically defined for all the supported formats.
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shellac
parents:
diff changeset
1813 [write_ps(), write_gif(), write_dia(), ...]
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shellac
parents:
diff changeset
1814
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shellac
parents:
diff changeset
1815 The encoding is passed to `open` [1].
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shellac
parents:
diff changeset
1816
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shellac
parents:
diff changeset
1817 [1] https://docs.python.org/3/library/functions.html#open
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shellac
parents:
diff changeset
1818 """
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shellac
parents:
diff changeset
1819 if prog is None:
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shellac
parents:
diff changeset
1820 prog = self.prog
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shellac
parents:
diff changeset
1821 if format == 'raw':
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shellac
parents:
diff changeset
1822 s = self.to_string()
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shellac
parents:
diff changeset
1823 if not PY3:
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shellac
parents:
diff changeset
1824 s = unicode(s)
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shellac
parents:
diff changeset
1825 with io.open(path, mode='wt', encoding=encoding) as f:
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shellac
parents:
diff changeset
1826 f.write(s)
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shellac
parents:
diff changeset
1827 else:
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shellac
parents:
diff changeset
1828 s = self.create(prog, format, encoding=encoding)
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shellac
parents:
diff changeset
1829 with io.open(path, mode='wb') as f:
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shellac
parents:
diff changeset
1830 f.write(s)
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shellac
parents:
diff changeset
1831 return True
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shellac
parents:
diff changeset
1832
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shellac
parents:
diff changeset
1833 def create(self, prog=None, format='ps', encoding=None):
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shellac
parents:
diff changeset
1834 """Creates and returns a binary image for the graph.
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shellac
parents:
diff changeset
1835
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shellac
parents:
diff changeset
1836 create will write the graph to a temporary dot file in the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1837 encoding specified by `encoding` and process it with the
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shellac
parents:
diff changeset
1838 program given by 'prog' (which defaults to 'twopi'), reading
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1839 the binary image output and return it as:
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shellac
parents:
diff changeset
1840
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shellac
parents:
diff changeset
1841 - `str` of bytes in Python 2
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shellac
parents:
diff changeset
1842 - `bytes` in Python 3
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shellac
parents:
diff changeset
1843
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shellac
parents:
diff changeset
1844 There's also the preferred possibility of using:
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shellac
parents:
diff changeset
1845
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shellac
parents:
diff changeset
1846 create_'format'(prog='program')
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shellac
parents:
diff changeset
1847
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shellac
parents:
diff changeset
1848 which are automatically defined for all the supported formats,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1849 for example:
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shellac
parents:
diff changeset
1850
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shellac
parents:
diff changeset
1851 - `create_ps()`
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shellac
parents:
diff changeset
1852 - `create_gif()`
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shellac
parents:
diff changeset
1853 - `create_dia()`
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shellac
parents:
diff changeset
1854
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shellac
parents:
diff changeset
1855 If 'prog' is a list, instead of a string,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1856 then the fist item is expected to be the program name,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1857 followed by any optional command-line arguments for it:
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shellac
parents:
diff changeset
1858
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shellac
parents:
diff changeset
1859 [ 'twopi', '-Tdot', '-s10' ]
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shellac
parents:
diff changeset
1860
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shellac
parents:
diff changeset
1861
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shellac
parents:
diff changeset
1862 @param prog: either:
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shellac
parents:
diff changeset
1863
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shellac
parents:
diff changeset
1864 - name of GraphViz executable that
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1865 can be found in the `$PATH`, or
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shellac
parents:
diff changeset
1866
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shellac
parents:
diff changeset
1867 - absolute path to GraphViz executable.
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shellac
parents:
diff changeset
1868
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shellac
parents:
diff changeset
1869 If you have added GraphViz to the `$PATH` and
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1870 use its executables as installed
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1871 (without renaming any of them)
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shellac
parents:
diff changeset
1872 then their names are:
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shellac
parents:
diff changeset
1873
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shellac
parents:
diff changeset
1874 - `'dot'`
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shellac
parents:
diff changeset
1875 - `'twopi'`
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shellac
parents:
diff changeset
1876 - `'neato'`
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shellac
parents:
diff changeset
1877 - `'circo'`
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shellac
parents:
diff changeset
1878 - `'fdp'`
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shellac
parents:
diff changeset
1879 - `'sfdp'`
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shellac
parents:
diff changeset
1880
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shellac
parents:
diff changeset
1881 On Windows, these have the notorious ".exe" extension that,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1882 only for the above strings, will be added automatically.
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shellac
parents:
diff changeset
1883
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shellac
parents:
diff changeset
1884 The `$PATH` is inherited from `os.env['PATH']` and
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1885 passed to `subprocess.Popen` using the `env` argument.
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shellac
parents:
diff changeset
1886
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shellac
parents:
diff changeset
1887 If you haven't added GraphViz to your `$PATH` on Windows,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1888 then you may want to give the absolute path to the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1889 executable (for example, to `dot.exe`) in `prog`.
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shellac
parents:
diff changeset
1890 """
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shellac
parents:
diff changeset
1891
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1892 if prog is None:
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shellac
parents:
diff changeset
1893 prog = self.prog
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shellac
parents:
diff changeset
1894
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1895 assert prog is not None
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shellac
parents:
diff changeset
1896
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shellac
parents:
diff changeset
1897 if isinstance(prog, (list, tuple)):
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shellac
parents:
diff changeset
1898 prog, args = prog[0], prog[1:]
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shellac
parents:
diff changeset
1899 else:
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shellac
parents:
diff changeset
1900 args = []
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shellac
parents:
diff changeset
1901
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shellac
parents:
diff changeset
1902 # temp file
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1903 tmp_fd, tmp_name = tempfile.mkstemp()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1904 os.close(tmp_fd)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1905 self.write(tmp_name, encoding=encoding)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1906 tmp_dir = os.path.dirname(tmp_name)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1907
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shellac
parents:
diff changeset
1908 # For each of the image files...
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1909 for img in self.shape_files:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1910 # Get its data
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1911 f = open(img, 'rb')
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1912 f_data = f.read()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1913 f.close()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1914 # And copy it under a file with the same name in
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1915 # the temporary directory
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1916 f = open(os.path.join(tmp_dir, os.path.basename(img)), 'wb')
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1917 f.write(f_data)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1918 f.close()
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shellac
parents:
diff changeset
1919
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shellac
parents:
diff changeset
1920 arguments = ['-T{}'.format(format), ] + args + [tmp_name]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1921
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1922 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1923 stdout_data, stderr_data, process = call_graphviz(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1924 program=prog,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1925 arguments=arguments,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1926 working_dir=tmp_dir,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1927 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1928 except OSError as e:
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shellac
parents:
diff changeset
1929 if e.errno == errno.ENOENT:
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shellac
parents:
diff changeset
1930 args = list(e.args)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1931 args[1] = '"{prog}" not found in path.'.format(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1932 prog=prog)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1933 raise OSError(*args)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1934 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1935 raise
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shellac
parents:
diff changeset
1936
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1937 # clean file litter
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1938 for img in self.shape_files:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1939 os.unlink(os.path.join(tmp_dir, os.path.basename(img)))
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shellac
parents:
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1940
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1941 os.unlink(tmp_name)
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1942
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1943 if process.returncode != 0:
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1944 message = (
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1945 '"{prog}" with args {arguments} returned code: {code}\n\n'
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1946 'stdout, stderr:\n {out}\n{err}\n'
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1947 ).format(
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1948 prog=prog,
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1949 arguments=arguments,
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1950 code=process.returncode,
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1951 out=stdout_data,
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1952 err=stderr_data,
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1953 )
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1954 print(message)
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1955
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1956 assert process.returncode == 0, (
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1957 '"{prog}" with args {arguments} returned code: {code}'.format(
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1958 prog=prog,
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1959 arguments=arguments,
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1960 code=process.returncode,
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1961 )
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1962 )
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1963
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1964 return stdout_data